The canonical enumeration of chemical structures has been broadly used as a kind of information index for chemical bibliography since computer entered into use in the field of chemistry. Moreover，it has also got many important uses in developing knowledge as-stems of chemistry. This review summarizes the basic principles of enumeration which are based on topological properties of the structure graphs and the methods of formation From these graphs.Then it analyzes the functions of this structure encoding in the chemical infermation system currently used，including bibliographic databases，chemical reaction databases ,and tlae: knowledge systems for molecular design and synthesis reaction-path plans.